Wise Clock 3 has 3 buttons, named (in the silkscreen on the board) "Menu", "Set" and "Plus". The "Menu" button is the rightmost one as you face the clock, "Set" is the middle button.

By pressing the "Menu" button, the menu options are shown at the top of the screen, in sequence. A menu option is selected by pressing the "Set" button. Some of the menu options (e.g. "Time", "Date") allow the user to set values, for example the time, the date etc. To increment these values, the user presses button "Plus".

1. Set up the time
- press "Menu" repeatedly until the option "TIME" is shown;
- press "Set": now, one of either hours or minutes will start blinking;
- press "Plus" to increment the blinking value; for hours, next value after 23 is 0; for minutes, next value after 59 is 0;
- to change between setting (blinking) hours and minutes, press "Set";
- after the desired time is set (values for hours and minutes are on display), wait about 4 seconds for the blinking to end; this is the time now stored by the clock.
Note: The value for seconds is always set to 0 every time the value for hours or minutes is incremented.

2. Set up the date
- press "Menu" repeatedly until the option "DATE" is shown;
- press "Set": the top part of the display will show "Y M D", and the bottom part will show the date, in the format "YYMMDD" (year/month/day);
- press "Plus" to increment the blinking value; for years, next value after 50 is 0; for months, next value after 12 is 1; for days, next value after 31 is 1;
- to change between setting (blinking) year, month and day, press "Set";
- after the desired date is set (values for year, month and day are on display), wait about 4 seconds for the blinking to end; this is the date now stored by the clock.

3. Set up the day-of-week
- press "Menu" repeatedly until the option "DAY" is shown;
- press "Set": now the bottom half of the display will show the first three letters of the day of the week (e.g. Mon, Tue etc);
- press "Plus" to increment the day;
- after the desired day is reached (shown on display), wait about 4 seconds and the "DAY" option will be exit automatically; this is the day now stored by the clock.

4. Set display brightness
Every time the "Set" button is pressed in one of the main display modes ("Quotes", "Pong", "Pacman", "Big"), the brightness of the LEDs increases one level (out of 5 levels); next after the highest brightness level is the lowest level.

5. Set quote scrolling speed
To increase the speed of the scrolling, press the "Plus" button when in the mode "Quote". There are 5 speeds. Next after the highest speed comes the slowest.

6. Display modes
Changing the display modes is done by pressing the "Menu" button, then selecting the mode shown by pressing the button "Set".
The main mode is "Quote", which displays scrolling quotations, read from SD card, on the half top of the screen.

Other modes are:
- "Pacman" - Pacman passes by every minute;
- "Pong" - as in the old-days tennis game console; hours and minutes are displayed on both sides of the net, at the top of the screen, and change when a player "loses", every minute, of course;
- "Big" - hours, minutes and seconds are displayed on the whole screen, in may different fonts;
- UTC (universal time), useful for radio amateurs;
- "Score" - allows keeping the game's score between two players, between 0 and 99.

7. Clock settings (options)
Beside the current time, Wise Clock 3 can also display:
- current date, formatted as "Month Day, Year"; this setting is enabled/disabled through the "DT+"/"DT-" menu options.
- temperature, in both Celsius and Fahrenheit; this setting is enabled/disabled through the "TEMP+"/"TEMP-" menu options.
- a personalized, user-editable message, read from SD card (e.g. "Happy Birthday dear John"); this setting is enabled/disabled through the "MESG+"/"MESG-" menu options.
- reminders for special events (anniversaries, Christmas etc), also user-editable on SD card; this setting is enabled/disabled through the "REMI+"/"REMI-" menu options.
- hours as maximum 12 or 24; this setting is enabled/disabled through the "24H+"/"24H-" menu options;
- enable/disable chime (short beep at the bottom of the hour, double beep at the top of the hour), by selecting "CHME+"/"CHME-" respectively.

Note: Menu will no longer show entries which do not make sense, like "DATE+" when the Date is already on.

8. Set up the alarm time
Alarm time can set through the menu option "ALARM". Press "Menu" button until you reach this option, then press "Set". From here on, the process is the same as setting up the time (point 2 above).

When alarm time is set and the alarm is active/enabled, the hours and minutes are separated by a colon, e.g. 15:43. If the alarm is disabled, a dot is used to separate the two, e.g. 15.43.

Another alarm-related feature: 3 hours before the alarm goes off, the time is displayed in orange, 2 hours before the alarm goes off in red; otherwise, time is displayed in green.

9. Enable/disable the alarm
The alarm is activated (will sound) only if the alarm is enabled. Enable/disable the alarm by selecting the "AL+"/"AL-" menu option.

When the alarm goes off, the clock plays "Frere Jacques", followed by a siren. The alarm can be stopped (silenced) by pressing any button.

10. Displaying reminders
At startup and at midnight the "message.txt" file is scanned for any reminder for that new day. An orange dot is displayed at the bottom during this scan. If a reminder is found then it will be displayed, like the quotes, for the next 24 hours.
The message file may also contain the start and end date of the Daylight Saving Time period (DST), this will adjust the clock by 1 hour.
The personal Message is still contained in this message file but must now start with [M1] which will allow for more then 1 Personal Message in a future release.
See message.txt for more details and add your own reminders.